index.Rmd

---
title: "Home"
site: workflowr::wflow_site
output:
  workflowr::wflow_html:
    toc: false
bibliography:
    - "`r here::here('data/references/references.bib')`"
---

```{r organoid-img, out.width = "40%", fig.align = "center", echo = FALSE}
knitr::include_graphics("organoid-black.png")
```

This website displays the analysis code and results for the analysis chapter of
my PhD thesis. In this chapter I reanalyse a previously published kidney
organoid scRNA-seq dataset [@Phipson2019-er; @Combes2019-uv], focusing on the 
decisions that are made during analysis and demonstrating a range of tools that
can be used for various tasks.

Follow the links below to access the different stages of analysis or refer to
the [Getting started](getting-started.html) page for more details about the
dataset and how to reproduce the analysis.

Analysis
========

* [Pre-processing](01-preprocessing.html) - Reading of datasets produced using
  Cell Ranger, comparison of droplet selection methods, annotation of the
  dataset.
* [Alevin](01B-alevin.html) - Comparison of the alignment-based dataset from
  Cell Ranger with the same data processed using the alevin method in Salmon.
* [Quality control](02-quality-control.html) - Selection of high-quality cells
  and removal of uninformative genes.
* [Clustering](03-clustering.html) - Clustering using the Seurat package with a
  comparison of methods for gene selection.
* [Marker genes](04-marker-genes.html) - Marker gene detection for each cluster
  using edgeR.
* [PAGA](05-paga.html) - Partition-based graph abstraction using the scanpy
  Python package with visualisation in R.
* [Cell velocity](06-velocyto.html) - Cell velocity estimates using the veloctyo
  package.

[Methods](90-methods.html) - Description of methods used during the analysis.

Citations
=========

This website and the analysis code can be cited as:

> Zappia, Luke. PhD thesis analysis. 2019.
> DOI:

This data files associated with this analysis can be cited as:

> Zappia L. PhD thesis analysis data. University of Melbourne. 2019.
> DOI: [10.26188/5c9182aa7e23d][figshare]

If you use this data in an analysis please cite the publcations that originally
described it.

References
==========

<div id="refs"></div>

[figshare]: https://melbourne.figshare.com/collections/PhD_thesis_analysis_data/4439804 "Figshare"

```{r session-info, eval = FALSE}
devtools::session_info()
```